RetrogeneDB ID: retro_rnor_1463

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:55240257..55240491(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000011065
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lsm2
• Ensembl ID: ENSRNOG00000048725
• Aliases: Lsm2, G7b
• Description: LSM2 homolog, U6 small nuclear RNA associated isoform 1 [Source:RefSeq peptide;Acc:NP_001004073]

Sequence

>retro_rnor_1463
CTCTTCTACTTCTTTTTCACGTCCCTTGTTGGCAAGGATGTAGTCGTAGAACTCAAGAATGGCCTGAGCATCTGTGGAAC
CCTCCACTCTGTGGACCAGTACCTCAATATCAAACTAACCGACATCAGTGTCACAGACCCTGAAAAGTATCCTCACATGT
TATCAGTCAAGAACTGCTTCATCAGGGGCTCGGTTGTCCAGTATGTGCAGCTGCCAGCAAACGAGGTGGACACA

Alignment

ORF - retro_rnor_1463 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.59 %
• Parental protein coverage: 59.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNCFIRGSVVRYVQ
          LFY.FF.SLVGKDVVVELKN.LSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNCFIRGSVV.YVQ
Retrocopy LFYFFFTSLVGKDVVVELKNGLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNCFIRGSVVQYVQ

Parental  LPADEVDT
          LPA.EVDT
Retrocopy LPANEVDT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	4.89 RPM
SRP017611_kidney	0.00 RPM	7.19 RPM
SRP017611_liver	0.00 RPM	4.50 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1463 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1463 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1463 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002601	2 retrocopies	retro_cjac_1828, retro_cjac_2088,
Felis catus	ENSFCAG00000004511	1 retrocopy	retro_fcat_309,
Macaca mulatta	ENSMMUG00000006832	3 retrocopies	retro_mmul_1389, retro_mmul_1875, retro_mmul_2099,
Mus musculus	ENSMUSG00000007050	1 retrocopy	retro_mmus_931,
Nomascus leucogenys	ENSNLEG00000006371	1 retrocopy	retro_nleu_960,
Ochotona princeps	ENSOPRG00000003668	2 retrocopies	retro_opri_250, retro_opri_917,
Pongo abelii	ENSPPYG00000016461	1 retrocopy	retro_pabe_2765,
Pan troglodytes	ENSPTRG00000017986	3 retrocopies	retro_ptro_1349, retro_ptro_2063, retro_ptro_2284,
Rattus norvegicus	ENSRNOG00000048725	1 retrocopy	retro_rnor_1463 ,
Ictidomys tridecemlineatus	ENSSTOG00000013144	1 retrocopy	retro_itri_189,